prof. UAM dr hab. Ewa Banachowicz

@article{Meier2018,

title = {Nano-viscosity of supercooled liquid measured by fluorescence correlation spectroscopy: Pressure and temperature dependence and the density scaling},

author = {G Meier and Jacek Gapiński and M Ratajczyk and M P Lettinga and K Hirtz and Ewa Banachowicz and Adam Patkowski},

url = {https://doi.org/10.1063/1.5011196},

doi = {10.1063/1.5011196},

year  = {2018},

date = {2018-01-01},

journal = {The Journal of Chemical Physics},

volume = {148},

number = {9},

pages = {094201},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Poznar2017,

title = {Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64)},

author = {Monika Poznar and Rafał Hołubowicz and Magdalena Wojtas and Jacek Gapiński and Ewa Banachowicz and Adam Patkowski and Andrzej Ożyhar and Piotr Dobryszycki},

url = {https://www.sciencedirect.com/science/article/pii/S1570963917302054?via%3Dihub http://linkinghub.elsevier.com/retrieve/pii/S1570963917302054},

doi = {10.1016/j.bbapap.2017.08.019},

issn = {15709639},

year  = {2017},

date = {2017-11-01},

journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},

volume = {1865},

number = {11},

pages = {1358--1371},

publisher = {Elsevier},

abstract = {Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Poatynska2017,

title = {Temperature dependent FCS studies using a long working distance objective: Viscosities of supercooled liquids and particle size},

author = {Agnieszka Połatyńska and Karolina Tomczyk and Mikołaj Pochylski and Gerd Meier and Jacek Gapiński and Ewa Banachowicz and Tomasz Śliwa and Adam Patkowski},

url = {http://aip.scitation.org/doi/10.1063/1.4977047},

doi = {10.1063/1.4977047},

issn = {00219606},

year  = {2017},

date = {2017-02-01},

journal = {Journal of Chemical Physics},

volume = {146},

number = {8},

pages = {084506},

publisher = {AIP Publishing LLC},

abstract = {In this work, we describe new experimental setups for Fluorescence Correlation Spectroscopy (FCS) where a long working distance objective is used. Using these setups, FCS measurements in a broad temperature range for a small sample volume of about 50 $mu$l can be performed. The use of specially designed cells and a dry long working distance objective was essential for avoiding temperature gradients in the sample. The performance of the new setups and a traditional FCS setup with immersion objectives is compared. The FCS data in combination with the Stokes-Einstein (SE) relation were used to obtain the values of the nanoviscosity of a fluid. We show for selected molecular van der Waals supercooled liquids that despite the fact that in these systems, a characteristic length scale can be defined, the nanoviscosity obtained from FCS is in a very good agreement with the macroscopic (rheometric) viscosity of the sample in a broad temperature range. This result corroborates the applicability of the SE relation to s...},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PCE:PCE12875,

title = {Solanum tuberosum ZPR1 encodes a light-regulated nuclear DNA-binding protein adjusting the circadian expression of StBBX24 to light cycle},

author = {Agnieszka Kiełbowicz-Matuk and Jagoda Czarnecka and Ewa Banachowicz and Pascal Rey and Tadeusz Rorat},

url = {http://dx.doi.org/10.1111/pce.12875},

doi = {10.1111/pce.12875},

issn = {1365-3040},

year  = {2017},

date = {2017-01-01},

journal = {Plant, Cell & Environment},

volume = {40},

number = {3},

pages = {424--440},

note = {PCE-16-0763.R1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kiebowicz-Matuk2016,

title = {Expression and characterization of a barley phosphatidylinositol transfer protein structurally homologous to the yeast Sec14p protein},

author = {Agnieszka Kiełbowicz-Matuk and Ewa Banachowicz and Anna Turska-Tarska and Pascal Rey and Tadeusz Rorat},

url = {http://linkinghub.elsevier.com/retrieve/pii/S0168945216300267},

doi = {10.1016/j.plantsci.2016.02.014},

issn = {01689452},

year  = {2016},

date = {2016-05-01},

journal = {Plant Science},

volume = {246},

pages = {98--111},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Banachowicz2014,

title = {Successful FCS Experiment in Nonstandard Conditions},

author = {Ewa Banachowicz and Adam Patkowski and Gerd Meier and Kamila Klamecka and Jacek Gapiński},

url = {http://pubs.acs.org/doi/10.1021/la5015708},

doi = {10.1021/la5015708},

issn = {0743-7463},

year  = {2014},

date = {2014-07-01},

journal = {Langmuir},

volume = {30},

number = {29},

pages = {8945--8955},

publisher = {American Chemical Society},

abstract = {Fluorescence correlation spectroscopy (FCS) is frequently used to measure the self-diffusion coefficient of fluorescently labeled probes in solutions, complex media, and living cells. In a standard experiment water immersion objectives and window thickness in the range of 0.13–0.19 mm are used. We show that successful FCS measurements can be performed using samples of different refractive index placed in cells having windows of different thickness, even much thicker than nominally allowed. Different water, oil, and silicon oil immersion as well as long working distance dry objectives, equipped with the correction collar, were tested and compared. We demonstrate that the requirements for FCS experiments are less stringent than those for high resolution confocal imaging and reliable relative FCS measurements can be performed even beyond the compensation range of the objectives. All these features open new possibilities for construction of custom-made high temperature and high pressure cells for FCS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Danielewicz-Ferchmin2013,

title = {Dielectric saturation in water as quantitative measure of formation of well-defined hydration shells of ions at various temperatures and pressures. Vapor–liquid equilibrium case},

author = {I Danielewicz-Ferchmin and Ewa Banachowicz and A R Ferchmin},

url = {https://www.sciencedirect.com/science/article/pii/S0167732213002079 http://linkinghub.elsevier.com/retrieve/pii/S0167732213002079},

doi = {10.1016/j.molliq.2013.06.005},

issn = {01677322},

year  = {2013},

date = {2013-11-01},

journal = {Journal of Molecular Liquids},

volume = {187},

pages = {157--164},

publisher = {Elsevier},

abstract = {Static electric permittivity ϵ of water at equilibrium saturated vapor pressures in electric field in the range 108textlessEtextless1011Vm−1 was calculated. A quantitative measure of the dielectric saturation phenomenon was introduced. It is found that, according to the definition of this measure, well-defined first hydration shells of numerous ions investigated by X-ray and neutron scattering methods described in literature are electrically saturated, and that at various conditions. Calculations show that around some ions, including Ag+, whose hydration shells are not saturated at ambient conditions, dielectric saturation of water can be achieved by increasing temperature and pressure up to the values not far from the critical ones. This is compared with extended X-ray absorption fine structure (EXAFS) and XAFS data for Ag+ and Rb+ found in literature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Danielewicz-Ferchmin2011,

title = {Role of electromechanical and mechanoelectric effects in protein hydration under hydrostatic pressure},

author = {Irena Danielewicz-Ferchmin and Ewa Banachowicz and Ryszard A Ferchmin},

url = {http://www.ncbi.nlm.nih.gov/pubmed/21897960 http://xlink.rsc.org/?DOI=c1cp21819k},

doi = {10.1039/c1cp21819k},

issn = {1463-9076},

year  = {2011},

date = {2011-10-01},

journal = {Physical Chemistry Chemical Physics},

volume = {13},

number = {39},

pages = {17722},

abstract = {Recent measurements of lysozyme hydration water density under non-denaturing pressure show that it is higher than that of bulk water in the same conditions. High protein hydration layer density has earlier been observed at ambient conditions and ascribed to electrostriction. We calculate the pressure-induced protein mean surface charge density increment $Delta$$sigma$. Within the hydration layer, the higher fields due to $Delta$$sigma$ lead to an additional water compression via electrostriction. The increment $Delta$$sigma$ is considered as due to a mechanoelectric effect in protein molecules. The mean value of the effective mechanoelectric coefficient d is calculated and compared with piezoelectric coefficients of amino acids and their compounds.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Banachowicz2009,

title = {High-pressure small-angle neutron scattering studies of glucose isomerase conformation in solution},

author = {Ewa Banachowicz and Maciej Kozak and Adam Patkowski and Gerhard Meier and Joachim Kohlbrecher},

url = {http://scripts.iucr.org/cgi-bin/paper?S0021889809007456},

doi = {10.1107/S0021889809007456},

issn = {0021-8898},

year  = {2009},

date = {2009-06-01},

journal = {Journal of Applied Crystallography},

volume = {42},

number = {3},

pages = {461--468},

publisher = {International Union of Crystallography},

abstract = {Small-angle neutron scattering (SANS) of solutions of glucose/xylose isomerase from Streptomyces rubiginosus was measured as a function of pressure. It is shown that the structure of the enzyme in solution as seen by SANS is practically the same as that in the crystal and does not change with pressure up to 150 MPa. This reflects the unusually high structural stability of this material, which makes it extremely interesting to use as a secondary standard for pressure-dependent SANS experiments. This lack of pressure dependence of the SANS data also indicates that any possible change in hydration of the protein induced by pressure is not visible in the SANS curves. An appropriate correction procedure must be used for the SANS data in order to account for the distortion of the intensity curve due to hard-sphere and electrostatic interactions. After this correction, the isomerase can be readily used as a secondary standard for SANS measurements.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Danielewicz-Ferchmin2007,

title = {Water phases under high electric field and pressure applied simultaneously},

author = {I Danielewicz-Ferchmin and Ewa Banachowicz and A R Ferchmin},

url = {https://www.sciencedirect.com/science/article/pii/S0167732207000074 http://linkinghub.elsevier.com/retrieve/pii/S0167732207000074},

doi = {10.1016/j.molliq.2006.10.006},

issn = {01677322},

year  = {2007},

date = {2007-07-01},

journal = {Journal of Molecular Liquids},

volume = {135},

number = {1-3},

pages = {75--85},

publisher = {Elsevier},

abstract = {The rigorous equation of state of an open system containing water in an electric field above 108 V m−1 under pressure applied in the range 10−4≤Po≤0.8 GPa leads to phase diagrams with two possible kinds of phase transitions at 293 K. The first one is the discontinuous phase transition under pressure applied in the range 10−4≤Po≤0.05 GPa in the $Pi$, $sigma$ coordinates ($Pi$ is the electrostriction pressure and $sigma$ denotes the surface charge density at an adjacent charged surface). The second one represents the continuous phase transition under pressure applied in the range 10−4≤Po≤0.8 GPa; it occurs at higher values of $sigma$ than the former one.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Danielewicz-Ferchmin2006,

title = {Properties of Hydration Shells of Protein Molecules at their Pressure- and Temperature-Induced Native-Denatured Transition},

author = {Irena Danielewicz-Ferchmin and Ewa Banachowicz and Ryszard A Ferchmin},

url = {http://www.ncbi.nlm.nih.gov/pubmed/16955512 http://doi.wiley.com/10.1002/cphc.200600289},

doi = {10.1002/cphc.200600289},

issn = {1439-4235},

year  = {2006},

date = {2006-10-01},

journal = {ChemPhysChem},

volume = {7},

number = {10},

pages = {2126--2133},

abstract = {Properties of water at the surface of biomolecules are important for their conformational stability. The behaviour of hydrating water at protein transition (t) pressures P(t) and temperatures T(t) , with the points (P(t),T(t) ) lying in the Native-Denatured (N-D) transition line, is studied. Hydration shells at the hydrophilic regions of protein molecules with surface charge density sigma are investigated with the help of the equation of state of water in an open system. The local values of sigma rather close to each other (sigma(D) approximately 0.3 C m(-2)) are found for six different experimental lines of the N-D transition found in the literature. The values sigma(D) correspond to the crossings of the total pressure (P(t)+Pi) vs sigma isotherms at different T(t) (Pi-electrostriction pressure). The pressures P(t) and temperatures T(t) appear to be related with some selected sites at the surfaces of the protein molecules.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hoffmann2006,

title = {Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors},

author = {Marcin Hoffmann and Krystian Eitner and Marcin von Grotthuss and Leszek Rychlewski and Ewa Banachowicz and Tomasz Grabarkiewicz and Tomasz Szkoda and Andrzej Kolinski},

url = {http://www.ncbi.nlm.nih.gov/pubmed/16972168 http://link.springer.com/10.1007/s10822-006-9057-z},

doi = {10.1007/s10822-006-9057-z},

issn = {0920-654X},

year  = {2006},

date = {2006-05-01},

journal = {Journal of Computer-Aided Molecular Design},

volume = {20},

number = {5},

pages = {305--319},

abstract = {The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Banachowicz2006a,

title = {Light scattering studies of proteins under compression},

author = {Ewa Banachowicz},

url = {http://www.ncbi.nlm.nih.gov/pubmed/16510323 http://linkinghub.elsevier.com/retrieve/pii/S157096390600032X},

doi = {10.1016/j.bbapap.2006.01.014},

issn = {15709639},

year  = {2006},

date = {2006-03-01},

journal = {Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics},

volume = {1764},

number = {3},

pages = {405--413},

abstract = {The scattering techniques are very convenient and effective in investigation of the shape, size and interactions of biological molecules close to their natural states in solution. However, it seems that from among a wide spectrum of scattering techniques, the light scattering ones have been relatively rarely used for the study of proteins under elevated hydrostatic pressure. This paper gives a brief description of the well developed possibilities of this technique for potential applications in the study of dissociation, aggregation and structural changes in proteins under compression. A short review of the already known applications is also given. Finally, the high-pressure dynamic light scattering results obtained by author on the lysozyme solution are shown and discussed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Banachowicz2006b,

title = {Static permittivity of water in electric field higher than 10 8 V m −1 and pressure varying from 0.1 to 600 MPa at room temperature},

author = {Ewa Banachowicz and I Danielewicz-Ferchmin},

url = {http://www.tandfonline.com/doi/abs/10.1080/00319100500338912},

doi = {10.1080/00319100500338912},

issn = {0031-9104},

year  = {2006},

date = {2006-02-01},

journal = {Physics and Chemistry of Liquids},

volume = {44},

number = {1},

pages = {95--105},

publisher = {Taylor & Francis Group},

abstract = {A recently proposed statistical approach to the permittivity $epsilon$ of water in the high electric field E (I. Danielewicz-Ferchmin, A.R. Ferchmin. Phys. Chem. Chem. Phys., 6, 1332 (2004)) has been applied to water at T = 293 K subjected to external pressure. Results are shown in the form of the set of isobars $epsilon$(E), which reveal abrupt falls at E∼109 V m−1.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Skibinska2004,

title = {Structural similarity ofE. coli 5S rRNA in solution and within the ribosome},

author = {Lidia Skibinska and Ewa Banachowicz and Jacek Gapiński and Adam Patkowski and Jan Barciszewski},

url = {http://doi.wiley.com/10.1002/bip.10598},

doi = {10.1002/bip.10598},

issn = {0006-3525},

year  = {2004},

date = {2004-02-01},

journal = {Biopolymers},

volume = {73},

number = {3},

pages = {316--325},

publisher = {Wiley Subscription Services, Inc., A Wiley Company},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jurga-Nowak2004,

title = {Supramolecular Guanosine 5 ′-Monophosphate Structures in Solution. Light Scattering Study},

author = {Hanna Jurga-Nowak and Ewa Banachowicz and Andrzej Dobek and Adam Patkowski},

url = {http://pubs.acs.org/doi/abs/10.1021/jp030905%2B},

doi = {10.1021/jp030905},

issn = {1520-6106},

year  = {2004},

date = {2004-01-01},

journal = {Journal of Physical Chemistry B},

volume = {108},

pages = {2744--2750},

publisher = {American Chemical Society},

abstract = {During the past decade, from the vast evidence it became clear that DNA oligomers rich in guanine stretches can form in solution highly ordered forms called G-quadruplexes and G-wires. G-quadruplexes are present in many sites of the human genome, can inhibit telomerase, and can be used as drug delivery supramolecules. G-wires and related structures seem to be an excellent material of biological origin for nanostructures. Therefore, in this paper we have studied the structures formed by specific association of guanosine 5‘-monophosphate (GMP) nucleotide molecules in water solutions by photon correlation spectroscopy and depolarized Rayleigh light scattering. One relaxation process with distinct amplitude was observed, as a function of temperature and sample concentration. It was attributed to the translational diffusion coefficient of the stacks of G-quartets in a range of high concentration and to the stacks of GMP monomer associates for low concentration (less than 40 mg/mL). From the measurements the hy...},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Danielewicz-Ferchmin2003,

title = {Protein hydration and the huge electrostriction},

author = {I Danielewicz-Ferchmin and Ewa Banachowicz and A R Ferchmin},

url = {http://www.ncbi.nlm.nih.gov/pubmed/14556903},

issn = {0301-4622},

year  = {2003},

date = {2003-11-01},

journal = {Biophysical chemistry},

volume = {106},

number = {2},

pages = {147--53},

abstract = {Recent experiments indicated the existence of hydration shells about biomolecules with densities markedly higher than that of bulk water. The compression is due to the pull of the dipoles of H(2)O molecules, necessary to achieve the thermodynamic equilibrium, from bulk water into the high field (approx. 10(9) V/m) region at the surface of the protein molecule. The electric field values at the surfaces of the biomolecules are calculated on the basis of the known densities. The reverse calculation of the limiting density values on the basis of known electric field distributions is performed, too. The results compare favourably with experiment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kaszynska2002,

title = {Dynamic Light Scattering and NMR Studies of Napin},

author = {Katarzyna Kaszyńska and Ewa Banachowicz and Genowefa Ślósarek and Adrian Morawiec and Iwona Gawrońska and Jan Barciszewski},

url = {http://link.springer.com/10.1023/A:1021877526536},

doi = {10.1023/A:1021877526536},

issn = {00959782},

year  = {2002},

date = {2002-01-01},

journal = {Journal of Solution Chemistry},

volume = {31},

number = {12},

pages = {987--993},

publisher = {Kluwer Academic Publishers-Plenum Publishers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Patkowski2000,

title = {Long-range density fluctuations in orthoterphenyl as studied by means of ultrasmall-angle x-ray scattering.},

author = {Adam Patkowski and T Thurn-Albrecht and Ewa Banachowicz and W Steffen and P Boesecke and T Narayanan and E W Fischer},

url = {http://www.ncbi.nlm.nih.gov/pubmed/11088383},

issn = {1063-651X},

year  = {2000},

date = {2000-06-01},

journal = {Physical review E},

volume = {61},

number = {6 Pt B},

pages = {6909--13},

abstract = {The structure factor of a fragile glass-forming liquid orthoterphenyl was measured in the previously inaccessible intermediate q range between the conventional light scattering (LS) and small-angle x-ray scattering (SAXS) q ranges using the low-angle scattering beam line at the European Synchrotron Radiation Facility. At low q the structure factor exhibits an excess scattering and matches well the LS data. This excess scattering is due to long-range density fluctuations also observed in the isotropic component of scattered light. At high q the structure factor decays to a plateau corresponding to the isothermal compressibility in agreement with the conventional SAXS data. In the intermediate q range, the structure factor exhibits a power law q dependence which indicates that the excess scattering is due to fractal aggregates of denser domains.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Banachowicz2000,

title = {Solution Structure of Biopolymers: A New Method of Constructing a Bead Model},

author = {Ewa Banachowicz and Jacek Gapiński and Adam Patkowski},

url = {http://www.ncbi.nlm.nih.gov/pubmed/10620274 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC1300618 http://linkinghub.elsevier.com/retrieve/pii/S0006349500765738},

doi = {10.1016/S0006-3495(00)76573-8},

issn = {00063495},

year  = {2000},

date = {2000-01-01},

journal = {Biophysical Journal},

volume = {78},

number = {1},

pages = {70--78},

publisher = {The Biophysical Society},

abstract = {We propose a new, automated method of converting crystallographic data into a bead model used for the calculations of hydrodynamic properties of rigid macromolecules. Two types of molecules are considered: nucleic acids and small proteins. A bead model of short DNA fragments has been constructed in which each nucleotide is represented by two identical, partially overlapping spheres: one for the base and one for the sugar and phosphate group. The optimum radius sigma = 5.0 A was chosen on the basis of a comparison of the calculated translational diffusion coefficients (D(T)) and the rotational relaxation times (tau(R)) with the corresponding experimental data for B-DNA fragments of 8, 12, and 20 basepairs. This value was assumed for the calculation D(T) and tau(R) of tRNA(Phe). Better agreement with the experimental data was achieved for slightly larger sigma = 5.7 A. A similar procedure was applied to small proteins. Bead models were constructed such that each amino acid was represented by a single sphere or a pair of identical, partially overlapping spheres, depending on the amino acid's size. Experimental data of D(T) of small proteins were used to establish the optimum value of sigma = 4.5 A for amino acids. The lack of experimental data on tau(R) for proteins restricted the tests to the translational diffusion properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}